
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   23 (  112),  selected   23 , name T0316TS102_5-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS102_5-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M     284           -
LGA    -       -      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    S     291      Y     313          2.120
LGA    Q     292      R     314           #
LGA    V     293      -       -           -
LGA    Y     313      Q     315          4.876
LGA    R     314      P     316          3.028
LGA    Q     315      D     317          3.760
LGA    P     316      S     318          0.753
LGA    -       -      K     319           -
LGA    D     317      V     320          2.472
LGA    S     318      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    -       -      E     330           -
LGA    K     319      V     331          3.331
LGA    V     320      I     332          4.028
LGA    V     322      F     333           #
LGA    T     329      A     334           -
LGA    E     330      E     335           -
LGA    -       -      P     336           -
LGA    -       -      Q     337           -
LGA    -       -      R     338           -
LGA    -       -      A     339           -
LGA    V     331      I     340          3.527
LGA    I     332      T     341          2.437
LGA    Y     349      P     342          2.774
LGA    -       -      G     343           -
LGA    -       -      Q     344           -
LGA    -       -      A     345           -
LGA    -       -      V     346           -
LGA    -       -      V     347           -
LGA    -       -      F     348           -
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    -       -      L     359           -
LGA    -       -      I     360           -
LGA    L     355      D     361          2.369
LGA    G     356      N     362          2.725
LGA    G     357      A     363          1.679
LGA    G     358      Y     364          1.422
LGA    L     359      R     365          3.651
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    I     360      C     370          3.863
LGA    -       -      Q     371           -
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23   90    5.0     17    3.05     0.00     11.652     0.540

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.386697 * X  +  -0.826206 * Y  +  -0.409693 * Z  +  77.143784
  Y_new =  -0.921466 * X  +  -0.363971 * Y  +  -0.135744 * Z  +  71.921394
  Z_new =  -0.036964 * X  +   0.430009 * Y  +  -0.902067 * Z  +  45.342918 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.696764   -0.444829  [ DEG:   154.5132    -25.4868 ]
  Theta =   0.036972    3.104620  [ DEG:     2.1184    177.8816 ]
  Phi   =  -1.173462    1.968131  [ DEG:   -67.2344    112.7656 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0316TS102_5-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS102_5-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23   90   5.0   17   3.05    0.00  11.652
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS102_5-D3
PFRMAT TS
TARGET T0316
MODEL 5
PARENT 1jcm_P
ATOM    649  N   SER   291      23.486  22.593  -1.618  1.00  1.00
ATOM    650  CA  SER   291      22.446  22.239  -2.591  1.00  1.00
ATOM    651  C   SER   291      22.660  21.021  -3.491  1.00  1.00
ATOM    652  O   SER   291      21.717  20.265  -3.741  1.00  1.00
ATOM    653  CB  SER   291      22.145  23.441  -3.491  1.00  1.00
ATOM    654  N   GLN   292      23.874  20.844  -4.008  1.00  1.00
ATOM    655  CA  GLN   292      24.164  19.712  -4.896  1.00  1.00
ATOM    656  C   GLN   292      23.757  18.399  -4.240  1.00  1.00
ATOM    657  O   GLN   292      23.500  17.406  -4.930  1.00  1.00
ATOM    658  CB  GLN   292      25.644  19.688  -5.260  1.00  1.00
ATOM    659  N   VAL   293      23.699  18.419  -2.906  1.00  1.00
ATOM    660  CA  VAL   293      23.308  17.263  -2.101  1.00  1.00
ATOM    661  C   VAL   293      21.856  17.327  -1.566  1.00  1.00
ATOM    662  O   VAL   293      21.075  16.383  -1.761  1.00  1.00
ATOM    663  CB  VAL   293      24.290  17.098  -0.939  1.00  1.00
ATOM    664  N   TYR   313      21.509  18.438  -0.910  1.00  1.00
ATOM    665  CA  TYR   313      20.172  18.659  -0.333  1.00  1.00
ATOM    666  C   TYR   313      19.042  18.611  -1.368  1.00  1.00
ATOM    667  O   TYR   313      17.881  18.400  -1.015  1.00  1.00
ATOM    668  CB  TYR   313      20.105  20.021   0.378  1.00  1.00
ATOM    669  N   ARG   314      19.374  18.807  -2.642  1.00  1.00
ATOM    670  CA  ARG   314      18.368  18.805  -3.701  1.00  1.00
ATOM    671  C   ARG   314      17.981  17.404  -4.159  1.00  1.00
ATOM    672  O   ARG   314      17.186  17.242  -5.084  1.00  1.00
ATOM    673  CB  ARG   314      18.867  19.621  -4.881  1.00  1.00
ATOM    674  N   GLN   315      18.538  16.384  -3.518  1.00  1.00
ATOM    675  CA  GLN   315      18.214  15.021  -3.913  1.00  1.00
ATOM    676  C   GLN   315      17.662  14.186  -2.777  1.00  1.00
ATOM    677  O   GLN   315      18.142  14.257  -1.642  1.00  1.00
ATOM    678  CB  GLN   315      19.438  14.324  -4.505  1.00  1.00
ATOM    679  N   PRO   316      16.648  13.388  -3.103  1.00  1.00
ATOM    680  CA  PRO   316      16.006  12.516  -2.133  1.00  1.00
ATOM    681  C   PRO   316      16.986  11.444  -1.664  1.00  1.00
ATOM    682  O   PRO   316      17.288  11.344  -0.472  1.00  1.00
ATOM    683  CB  PRO   316      14.778  11.864  -2.756  1.00  1.00
ATOM    684  N   ASP   317      17.475  10.631  -2.599  1.00  1.00
ATOM    685  CA  ASP   317      18.441   9.604  -2.243  1.00  1.00
ATOM    686  C   ASP   317      19.707  10.386  -1.944  1.00  1.00
ATOM    687  O   ASP   317      20.497  10.678  -2.839  1.00  1.00
ATOM    688  CB  ASP   317      18.685   8.653  -3.414  1.00  1.00
ATOM    689  N   SER   318      19.882  10.740  -0.682  1.00  1.00
ATOM    690  CA  SER   318      21.038  11.516  -0.269  1.00  1.00
ATOM    691  C   SER   318      22.372  10.781  -0.386  1.00  1.00
ATOM    692  O   SER   318      23.396  11.410  -0.630  1.00  1.00
ATOM    693  CB  SER   318      20.849  12.007   1.166  1.00  1.00
ATOM    694  N   LYS   319      22.368   9.462  -0.211  1.00  1.00
ATOM    695  CA  LYS   319      23.609   8.694  -0.301  1.00  1.00
ATOM    696  C   LYS   319      24.084   8.601  -1.753  1.00  1.00
ATOM    697  O   LYS   319      25.281   8.717  -2.039  1.00  1.00
ATOM    698  CB  LYS   319      23.417   7.288   0.294  1.00  1.00
ATOM    699  N   VAL   320      23.134   8.399  -2.663  1.00  1.00
ATOM    700  CA  VAL   320      23.440   8.301  -4.083  1.00  1.00
ATOM    701  C   VAL   320      23.986   9.648  -4.566  1.00  1.00
ATOM    702  O   VAL   320      24.814   9.710  -5.477  1.00  1.00
ATOM    703  CB  VAL   320      22.175   7.920  -4.863  1.00  1.00
ATOM    704  N   VAL   322      23.531  10.726  -3.933  1.00  1.00
ATOM    705  CA  VAL   322      23.966  12.071  -4.300  1.00  1.00
ATOM    706  C   VAL   322      25.423  12.298  -3.926  1.00  1.00
ATOM    707  O   VAL   322      26.165  12.931  -4.668  1.00  1.00
ATOM    708  CB  VAL   322      23.080  13.123  -3.619  1.00  1.00
ATOM    709  N   THR   329      25.826  11.783  -2.770  1.00  1.00
ATOM    710  CA  THR   329      27.194  11.944  -2.306  1.00  1.00
ATOM    711  C   THR   329      28.133  11.127  -3.166  1.00  1.00
ATOM    712  O   THR   329      29.283  11.512  -3.384  1.00  1.00
ATOM    713  CB  THR   329      27.339  11.536  -0.832  1.00  1.00
ATOM    714  N   GLU   330      27.637  10.002  -3.663  1.00  1.00
ATOM    715  CA  GLU   330      28.446   9.156  -4.524  1.00  1.00
ATOM    716  C   GLU   330      28.703   9.832  -5.872  1.00  1.00
ATOM    717  O   GLU   330      29.826   9.806  -6.375  1.00  1.00
ATOM    718  CB  GLU   330      27.773   7.787  -4.702  1.00  1.00
ATOM    719  N   VAL   331      27.671  10.451  -6.445  1.00  1.00
ATOM    720  CA  VAL   331      27.807  11.135  -7.729  1.00  1.00
ATOM    721  C   VAL   331      28.699  12.378  -7.670  1.00  1.00
ATOM    722  O   VAL   331      29.646  12.513  -8.444  1.00  1.00
ATOM    723  CB  VAL   331      26.438  11.589  -8.264  1.00  1.00
ATOM    724  N   ILE   332      28.372  13.278  -6.745  1.00  1.00
ATOM    725  CA  ILE   332      29.054  14.561  -6.587  1.00  1.00
ATOM    726  C   ILE   332      30.404  14.570  -5.888  1.00  1.00
ATOM    727  O   ILE   332      31.312  15.283  -6.302  1.00  1.00
ATOM    728  CB  ILE   332      28.111  15.568  -5.887  1.00  1.00
ATOM    729  N   TYR   349      30.542  13.791  -4.828  1.00  1.00
ATOM    730  CA  TYR   349      31.804  13.755  -4.114  1.00  1.00
ATOM    731  C   TYR   349      32.747  12.669  -4.614  1.00  1.00
ATOM    732  O   TYR   349      33.960  12.870  -4.674  1.00  1.00
ATOM    733  CB  TYR   349      31.549  13.566  -2.624  1.00  1.00
ATOM    734  N   LEU   355      32.194  11.522  -4.992  1.00  1.00
ATOM    735  CA  LEU   355      33.023  10.422  -5.445  1.00  1.00
ATOM    736  C   LEU   355      33.106  10.238  -6.948  1.00  1.00
ATOM    737  O   LEU   355      33.877   9.409  -7.424  1.00  1.00
ATOM    738  CB  LEU   355      32.529   9.123  -4.818  1.00  1.00
ATOM    739  N   GLY   356      32.328  11.001  -7.701  1.00  1.00
ATOM    740  CA  GLY   356      32.350  10.832  -9.142  1.00  1.00
ATOM    741  C   GLY   356      32.004   9.384  -9.397  1.00  1.00
ATOM    742  O   GLY   356      32.494   8.754 -10.335  1.00  1.00
ATOM    743  N   GLY   357      31.148   8.864  -8.527  1.00  1.00
ATOM    744  CA  GLY   357      30.707   7.487  -8.598  1.00  1.00
ATOM    745  C   GLY   357      29.463   7.364  -9.454  1.00  1.00
ATOM    746  O   GLY   357      29.202   8.227 -10.290  1.00  1.00
ATOM    747  N   GLY   358      28.693   6.298  -9.229  1.00  1.00
ATOM    748  CA  GLY   358      27.486   6.015 -10.010  1.00  1.00
ATOM    749  C   GLY   358      27.869   6.209 -11.474  1.00  1.00
ATOM    750  O   GLY   358      27.018   6.434 -12.337  1.00  1.00
ATOM    751  N   LEU   359      29.173   6.098 -11.726  1.00  1.00
ATOM    752  CA  LEU   359      29.748   6.265 -13.050  1.00  1.00
ATOM    753  C   LEU   359      29.058   7.439 -13.726  1.00  1.00
ATOM    754  O   LEU   359      28.704   7.375 -14.903  1.00  1.00
ATOM    755  CB  LEU   359      29.580   4.974 -13.866  1.00  1.00
ATOM    756  N   ILE   360      28.872   8.504 -12.944  1.00  1.00
ATOM    757  CA  ILE   360      28.229   9.752 -13.361  1.00  1.00
ATOM    758  C   ILE   360      26.722   9.741 -13.078  1.00  1.00
ATOM    759  O   ILE   360      26.214  10.754 -12.551  1.00  1.00
ATOM    760  CB  ILE   360      28.484  10.068 -14.869  1.00  1.00
TER
END
